Hi again! Thank you for being so prompt with the answers. I appreciate it.
Question, if my read length is 101 bp, should I use bowtie2 instead of bowtie? I have been using bowtie to map the reads as most of the tutorials use bowtie, however the length of their reads is usually 36. I have been getting good results (I assume, it generates apprx. 31000000 lines) with bowtie, but I was wondering if bowtie2 is the proper program to use and whether the results could be different. Also, for the map with BWA (the one that galaxy has a tutorial on, with the two replicates), there is no built in arabidopsis genome. Does that mean I cannot use it to do the mapping?
Thanks again!